Why is BLAST used in primer design? Primer-BLAST allows for the construction of primers for qPCR where the user can specify the melting temperature, reduce the amount of self-priming, and span exon-exon junctions in order to avoid amplification of contaminating genomic DNA.
What makes a primer more suitable for PCR? A good length for PCR primers is generally around 18-30 bases. Specificity usually is dependent on length and annealing temperature. The shorter the primers are, the more efficiently they will bind or anneal to the target.
Why do we use primers in qPCR? Primers can be combined with DNA-binding dyes in amplification reactions to monitor the appearance of double-stranded DNA (dsDNA). However, fluorescently labeled probes can be used for greater specificity in a qPCR assay.
Why is primer design important? The primer design is an important step to get an optimal PCR. If you pick up primers without design, the amplification may not work or give you “strange” results, for example if the primer can hybridize at another position in the genome.